Title: Performance modelling of parallel BLAST using Intel and PGI compilers on an infiniband-based HPC cluster

Authors: Muhammed Al-Mulhem; Raed Al-Shaikh

Addresses: Information and Computer Science Department, King Fahd University of Petroleum & Minerals (KFUPM), Dhahran 31261, Saudi Arabia ' EXPEC Computer Center, Saudi Aramco, Dhahran 31311, Saudi Arabia

Abstract: The Basic Local Alignment Search (BLAST) is one of the most widely used bioinformatics programs for searching all available sequence databases for similarities between a protein or DNA query and predefined sequences, using sequence alignment technique. Recently, many attempts have been made to make the algorithm practical to run against the publicly available genome databases. This paper presents our experience in mapping and evaluating both the serial and parallel BLAST algorithms onto a large Infiniband-based High Performance Cluster. The evaluation is performed using two commonly used parallel compilers, Intel and Portland's PGI. The paper also presents the evaluation methodology along with the experimental results to illustrate the scalability of the BLAST algorithm on our state-of-the-art HPC system. Our results show that BLAST runtime scalability can be achieved with up to 87% efficiency when considering the right combination of the MPI suite, the parallel compiler, the cluster interconnect and the CPU technology.

Keywords: parallel BLAST; bioinformatics; genomes; HPC clusters; Intel; PGI compilers; infiniband; performance evaluation; modelling; sequence alignment; high performance computing.

DOI: 10.1504/IJBRA.2013.056086

International Journal of Bioinformatics Research and Applications, 2013 Vol.9 No.5, pp.534 - 546

Received: 23 Mar 2011
Accepted: 10 Oct 2011
Published online: 18 Sep 2014 *

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